Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate RR42_RS29445 RR42_RS29445 ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__Cup4G11:RR42_RS29445 Length = 358 Score = 155 bits (392), Expect = 2e-42 Identities = 101/331 (30%), Positives = 172/331 (51%), Gaps = 38/331 (11%) Query: 15 LLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALM 74 LL+ P S+ W+ L+Y + LGL ++ GY GLL +G+ AF VGAY A + Sbjct: 32 LLIAPGWASSY---WIAQLGFVLIYAIAGLGLMVLSGYTGLLSIGHAAFLGVGAYTQAWL 88 Query: 75 ASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLG 134 S H A A AA L+A G ++G P L+++G YLAI TL Sbjct: 89 TS-HGVPFVPALLA----------------AAALSALTGVVVGLPALRVKGIYLAIATLA 131 Query: 135 FGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFL 194 FG I+ L + ++T G GL +++G+ ++ +YYL L Sbjct: 132 FGLIVEEILARWE---SVTGGNAGLPVAAP------------QLWGYVLDGPVAFYYLSL 176 Query: 195 VLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAM 254 + +++ + L S GRA++AIR+ EI+A++MGI+ K L+F + A+ G++GA+ Sbjct: 177 AVCLLATLAVLNLLRSATGRAFIAIRDSEISAQSMGIHLARYKTLSFALSAALVGIAGAL 236 Query: 255 FGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAM 314 + ++SPE F + +S+ ++ +VV+GG+G + G LGA+ L +P+++ +A L Sbjct: 237 YAHKLRYISPEQFGIAQSIDLLLLVVVGGLGSVHGAFLGAIFLIVMPQMI-VLAKDLLPP 295 Query: 315 TDGRLDSAILRQLLIALAMIIIMLLRPRGLW 345 G+ ++ L+ L ++ +L P GL+ Sbjct: 296 AIGQASG--MQALVYGLVLMAFVLFEPMGLY 324 Lambda K H 0.328 0.144 0.430 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 298 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 358 Length adjustment: 29 Effective length of query: 329 Effective length of database: 329 Effective search space: 108241 Effective search space used: 108241 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory